ILT3-binding agents and methods of use thereof

Abstract

The present disclosure provides binding agents, such as antibodies, that specifically bind ILT3, including human ILT3, as well as compositions comprising the binding agents, and methods of their use. The disclosure also provides related polynucleotides and vectors encoding the binding agents and cells comprising the binding agents.

What is claimed: 
     
       1. An antibody that specifically binds human immunoglobulin-like transcript 3 (ILT3), wherein the antibody comprises:
 (a) a heavy chain variable region (VH) comprising a VH-complementarity determining region (CDR)1, a VH-CDR2, and a VH-CDR3 from the amino acid sequence of SEQ ID NO:111; and a light chain variable region (VL) comprising a VL-complementarity determining region (CDR)1, a VL-CDR2, and a VL-CDR3 from the amino acid sequence of SEQ ID NO:112; or 
 (b) a VH comprising a VH-CDR1, a VH-CDR2, and a VH-CDR3 from the amino acid sequence of SEQ ID NO:123; and a VL comprising a VL-CDR1, a VL-CDR2, and a VL-CDR3 from the amino acid sequence of SEQ ID NO:124. 
 
     
     
       2. The antibody of  claim 1 , wherein:
 (a) the VH-CDR1 comprises the amino acid sequence GFTFSSYGMS (SEQ ID NO:27), the VH-CDR2 comprises the amino acid sequence TISGGGSYTNYPDSVKG (SEQ ID NO:28), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (b) the VH-CDR1 comprises the amino acid sequence GFTFSSY (SEQ ID NO:33), the VH-CDR2 comprises the amino acid sequence SGGGSY (SEQ ID NO:34), the VH CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (c) the VH-CDR1 comprises the amino acid sequence GFTFSSYGMS (SEQ ID NO:27), the VH-CDR2 comprises the amino acid sequence TISGGGSYTN (SEQ ID NO:35), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (d) the VH CDR1 comprises the amino acid sequence SYGMS (SEQ ID NO:36), the VH-CDR2 comprises the amino acid sequence TISGGGSYTNYPDSVKG (SEQ ID NO:28), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (e) the VH-CDR1 comprises the amino acid sequence SSYGMS (SEQ ID NO:37), the VH-CDR2 comprises the amino acid sequence WVATISGGGSYTN (SEQ ID NO:38), the VH-CDR3 comprises the amino acid sequence ARREWRYTLYAMD (SEQ ID NO:107), the VL-CDR1 comprises the amino acid sequence ESYGSSFMHWY (SEQ ID NO:108), the VL-CDR2 comprises the amino acid sequence LLIYLTSNLE (SEQ ID NO:41), and the VL-CDR3 comprises the amino acid sequence QQNNEDPF (SEQ ID NO:42), 
 (f) the VH-CDR1 comprises the amino acid sequence GFTFSSYGMS (SEQ ID NO:27), the VH-CDR2 comprises the amino acid sequence TISGGGSYTNYPDSVKG (SEQ ID NO:28), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:29), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:30), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (g) the VH-CDR1 comprises the amino acid sequence GFTFSSY (SEQ ID NO:33), the VH-CDR2 comprises the amino acid sequence SGGGSY (SEQ ID NO:34), the VH CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:29), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:30), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (h) the VH-CDR1 comprises the amino acid sequence GFTFSSYGMS (SEQ ID NO:27), the VH-CDR2 comprises the amino acid sequence TISGGGSYTN (SEQ ID NO:35), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:29), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:30), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (i) the VH CDR1 comprises the amino acid sequence SYGMS (SEQ ID NO:36), the VH-CDR2 comprises the amino acid sequence TISGGGSYTNYPDSVKG (SEQ ID NO:28), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:29), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:30), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); or 
 (j) the VH-CDR1 comprises the amino acid sequence SSYGMS (SEQ ID NO:37), the VH-CDR2 comprises the amino acid sequence WVATISGGGSYTN (SEQ ID NO:38), the VH-CDR3 comprises the amino acid sequence ARREWRMTLYAMD (SEQ ID NO:39), the VL-CDR1 comprises the amino acid sequence DSYGNSFMHWY (SEQ ID NO:40), a VL-CDR2 comprises the amino acid sequence LLIYLTSNLE (SEQ ID NO:41), and the VL-CDR3 comprises the amino acid sequence QQNNEDPF (SEQ ID NO:42). 
 
     
     
       3. The antibody of  claim 1 , wherein:
 (a) the VH comprises the amino acid sequence of SEQ ID NO:123 and/or the VL comprises the amino acid sequence of SEQ ID NO:124; or 
 (b) the VH comprises the amino acid sequence of SEQ ID NO:111 and/or the VL comprises the amino acid sequence of SEQ ID NO:112. 
 
     
     
       4. The antibody of  claim 1 , wherein the antibody is a chimeric antibody, a recombinant antibody, a humanized antibody, a bispecific antibody, or a multispecific antibody. 
     
     
       5. The antibody of  claim 1 , wherein the antibody is an antibody fragment comprising at least one antigen-binding site. 
     
     
       6. The antibody of  claim 5 , wherein the antibody fragment is a Fab, a Fab′, a F(ab′) 2 , a Fv, an scFv, an (scFv) 2 , a single chain antibody, a dual variable region antibody, a diabody, or a nanobody. 
     
     
       7. The antibody of  claim 1 , wherein the antibody is an IgG1 antibody, an IgG2 antibody, or an IgG4 antibody. 
     
     
       8. The antibody of  claim 1 , comprising a kappa light chain constant region or a lambda light chain constant region. 
     
     
       9. The antibody of  claim 1 , comprising a human IgG1 constant region and a human kappa light chain constant region. 
     
     
       10. The antibody of  claim 9 , wherein the human IgG1 constant region comprises one or more mutations that reduce or eliminate effector functions. 
     
     
       11. The antibody of  claim 1 , wherein the antibody is attached to a half-life extending moiety. 
     
     
       12. The antibody of  claim 1 , wherein the antibody has one or more of the following properties:
 (i) binding cynomolgus ILT3; 
 (ii) binding human and cynomolgus ILT3; 
 (iii) not binding ILT2, ILT4, ILT5, and or LILRB5; 
 (iv) not binding LILRA1, LILRA2, LILRA4, LILRA5, and or LILRA6; 
 (v) being an ILT3 antagonist; 
 (vi) inhibiting ILT3 activity; 
 (vii) inhibiting ILT3 signaling in cells that express ILT3; 
 (viii) inhibiting binding of ILT3 to APOE; 
 (ix) inhibiting binding of ILT3 to fibronectin; 
 (x) inhibiting binding of ILT3 to CNTFR; 
 (xi) inhibiting ILT3-induced suppression of myeloid cells; 
 (xii) inhibiting ILT3-induced suppression of myeloid cell activity; 
 (xiii) restoring FcR activation in myeloid cells that express ILT3; and 
 (xiv) restoring chemokine production in myeloid cells that express ILT3. 
 
     
     
       13. The antibody of  claim 12 , wherein the antibody has a K D  for human ILT3 of from 1 μM to 1 μM as assessed by Surface Plasmon Resonance (SPR). 
     
     
       14. The antibody of  claim 1 , comprising a heavy chain comprising the amino acid sequence of SEQ ID NO:126 and/or a light chain comprising the amino acid sequence of SEQ ID NO:128. 
     
     
       15. A pharmaceutical composition comprising the antibody of  claim 1  and a pharmaceutically acceptable carrier. 
     
     
       16. An isolated polynucleotide or polynucleotides encoding the antibody of  claim 1 . 
     
     
       17. A vector or vectors comprising the polynucleotide or polynucleotides of  claim 16 . 
     
     
       18. An isolated cell comprising the polynucleotide or polynucleotides of  claim 16 , or a vector or vectors comprising the polynucleotide or polynucleotides of  claim 16 . 
     
     
       19. A method of making an antibody that specifically binds human ILT3, the method comprising:
 (a) culturing the cell of  claim 18  under conditions that result in the expression of the antibody, and 
 (b) isolating the antibody. 
 
     
     
       20. The method of  claim 19 , further comprising formulating the antibody as a sterile pharmaceutical composition. 
     
     
       21. A method of disrupting, inhibiting, or blocking the binding of ILT3 to fibronectin or fibronectin-induced ILT3 activity in a mixture of cells, the method comprising contacting the cells with the antibody of  claim 1 . 
     
     
       22. A method of disrupting, inhibiting, or blocking ILT3-induced suppression of myeloid cells or ILT3-induced suppression of myeloid cell activity, the method comprising contacting the myeloid cells with the antibody of  claim 1 . 
     
     
       23. A method of disrupting, inhibiting, or blocking the binding of ILT3 to fibronectin or fibronectin-induced ILT3 activity in a subject, the method comprising administering to the subject a therapeutically effective amount of the antibody of  claim 1 . 
     
     
       24. A method of disrupting, inhibiting, or blocking ILT3-induced suppression of myeloid cells or ILT3-induced suppression of myeloid cell activity in a subject, the method comprising administering to the subject the antibody of  claim 1  in an amount sufficient to activate the myeloid cells. 
     
     
       25. A method of treating cancer, or inhibiting tumor growth, tumor relapse, or tumor regrowth in a subject, the method comprising administering to the subject a therapeutically effective amount of the antibody of  claim 1 . 
     
     
       26. A method of increasing or enhancing an immune response to a tumor or tumor cells in a subject, the method comprising administering to the subject a therapeutically effective amount of the antibody of  claim 1 . 
     
     
       27. A method of activating myeloid cells in the tumor microenvironment in a subject with a tumor, the method comprising administering to the subject a therapeutically effective amount of the antibody of  claim 1 . 
     
     
       28. The method of  claim 25 , wherein (i) the cancer is pancreatic cancer, breast cancer, lung cancer, head and neck cancer, colorectal cancer, prostate cancer, skin cancer, melanoma, stomach cancer, gastric cancer, intestinal cancer, ovarian cancer, cervical cancer, uterine cancer, endometrial cancer, urinary bladder cancer, brain cancer, esophageal cancer, liver cancer, kidney cancer, sarcoma, or testicular cancer; and/or (ii) the tumor is a pancreatic tumor, a breast tumor, a lung tumor, a head and neck tumor, a colorectal tumor, a prostate tumor, a skin tumor, a melanoma tumor, a stomach tumor, a gastric tumor, an intestinal tumor, an ovarian tumor, a cervical tumor, an uterine tumor, an endometrial tumor, a bladder tumor, a brain tumor, an esophageal tumor, a liver tumor, a kidney tumor, a sarcoma, or a testicular tumor. 
     
     
       29. The method of  claim 25 , wherein the cancer is hematologic cancer. 
     
     
       30. The method of  claim 29 , wherein the hematologic cancer is myelogenous leukemia, acute myeloid leukemia (AML), chronic myeloid leukemia, or myelodysplastic syndrome. 
     
     
       31. The method of  claim 26 , wherein the tumor is a pancreatic tumor, a breast tumor, a lung tumor, a head and neck tumor, a colorectal tumor, a prostate tumor, a skin tumor, a melanoma tumor, a stomach tumor, a gastric tumor, an intestinal tumor, an ovarian tumor, a cervical tumor, an uterine tumor, an endometrial tumor, a bladder tumor, a brain tumor, an esophageal tumor, a liver tumor, a kidney tumor, a sarcoma, or a testicular tumor. 
     
     
       32. The method of  claim 27 , wherein the tumor is a pancreatic tumor, a breast tumor, a lung tumor, a head and neck tumor, a colorectal tumor, a prostate tumor, a skin tumor, a melanoma tumor, a stomach tumor, a gastric tumor, an intestinal tumor, an ovarian tumor, a cervical tumor, an uterine tumor, an endometrial tumor, a bladder tumor, a brain tumor, an esophageal tumor, a liver tumor, a kidney tumor, a sarcoma, or a testicular tumor. 
     
     
       33. The method of  claim 23 , wherein the antibody is administered as part of a combination therapy comprising a PD-1 antagonist. 
     
     
       34. The method of  claim 24 , wherein the antibody is administered as part of a combination therapy comprising a PD-1 antagonist. 
     
     
       35. The method of  claim 25 , wherein the antibody is administered as part of a combination therapy comprising a PD-1 antagonist. 
     
     
       36. The method of  claim 26 , wherein the antibody is administered as part of a combination therapy comprising a PD-1 antagonist. 
     
     
       37. The method of  claim 27 , wherein the antibody is administered as part of a combination therapy comprising a PD-1 antagonist. 
     
     
       38. The method of  claim 33 , wherein the PD-1 antagonist is pembrolizumab. 
     
     
       39. The method of  claim 34 , wherein the PD-1 antagonist is pembrolizumab. 
     
     
       40. The method of  claim 35 , wherein the PD-1 antagonist is pembrolizumab. 
     
     
       41. The method of  claim 36 , wherein the PD-1 antagonist is pembrolizumab. 
     
     
       42. The method of  claim 37 , wherein the PD-1 antagonist is pembrolizumab. 
     
     
       43. An antibody that specifically binds human ILT3, wherein the antibody comprises a VH comprising a VH-CDR1, a VH-CDR2, and a VH-CDR3 from the amino acid sequence of SEQ ID NO:123; and a VL comprising a VL-CDR1, a VL-CDR2, and a VL-CDR3 from the amino acid sequence of SEQ ID NO:124. 
     
     
       44. The antibody of  claim 43 , wherein:
 (a) the VH-CDR1 comprises the amino acid sequence GFTFSSYGMS (SEQ ID NO:27), the VH-CDR2 comprises the amino acid sequence TISGGGSYTNYPDSVKG (SEQ ID NO:28), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (b) the VH-CDR1 comprises the amino acid sequence GFTFSSY (SEQ ID NO:33), the VH-CDR2 comprises the amino acid sequence SGGGSY (SEQ ID NO:34), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (c) the VH-CDR1 comprises the amino acid sequence GFTFSSYGMS (SEQ ID NO:27), the VH-CDR2 comprises the amino acid sequence TISGGGSYTN (SEQ ID NO:35), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); 
 (d) the VH-CDR1 comprises the amino acid sequence SYGMS (SEQ ID NO:36), the VH-CDR2 comprises the amino acid sequence TISGGGSYTNYPDSVKG (SEQ ID NO:28), the VH-CDR3 comprises the amino acid sequence REWRYTLYAMDY (SEQ ID NO:105), the VL-CDR1 comprises the amino acid sequence RASESVESYGSSFMH (SEQ ID NO:106), the VL-CDR2 comprises the amino acid sequence LTSNLES (SEQ ID NO:31), and the VL-CDR3 comprises the amino acid sequence QQNNEDPFT (SEQ ID NO:32); or 
 (e) the VH-CDR1 comprises the amino acid sequence SSYGMS (SEQ ID NO:37), the VH-CDR2 comprises the amino acid sequence WVATISGGGSYTN (SEQ ID NO:38), the VH-CDR3 comprises the amino acid sequence ARREWRYTLYAMD (SEQ ID NO:107), the VL-CDR1 comprises the amino acid sequence ESYGSSFMHWY (SEQ ID NO:108), the VL-CDR2 comprises the amino acid sequence LLIYLTSNLE (SEQ ID NO:41), and the VL-CDR3 comprises the amino acid sequence QQNNEDPF (SEQ ID NO:42). 
 
     
     
       45. The antibody of  claim 43 , wherein the VH comprises the amino acid sequence of SEQ ID NO:123 and the VL comprises the amino acid sequence of SEQ ID NO:124. 
     
     
       46. The antibody of  claim 43 , comprising a heavy chain comprising the amino acid sequence of SEQ ID NO:126 and a light chain comprising the amino acid sequence of SEQ ID NO:128. 
     
     
       47. A method of treating cancer, or inhibiting tumor growth, tumor relapse, or tumor regrowth in a subject, comprising administering to the subject a therapeutically effective amount of the antibody of  claim 43 . 
     
     
       48. The method of  claim 47 , wherein (i) the cancer is pancreatic cancer, breast cancer, lung cancer, head and neck cancer, colorectal cancer, prostate cancer, skin cancer, melanoma, stomach cancer, gastric cancer, intestinal cancer, ovarian cancer, cervical cancer, uterine cancer, endometrial cancer, urinary bladder cancer, brain cancer, esophageal cancer, liver cancer, kidney cancer, sarcoma, or testicular cancer; and/or (ii) the tumor is a pancreatic tumor, a breast tumor, a lung tumor, a head and neck tumor, a colorectal tumor, a prostate tumor, a skin tumor, a melanoma tumor, a stomach tumor, a gastric tumor, an intestinal tumor, an ovarian tumor, a cervical tumor, an uterine tumor, an endometrial tumor, a bladder tumor, a brain tumor, an esophageal tumor, a liver tumor, a kidney tumor, a sarcoma, or a testicular tumor. 
     
     
       49. The method of  claim 47 , wherein the cancer is hematologic cancer. 
     
     
       50. The method of  claim 49 , wherein the hematologic cancer is myelogenous leukemia, acute myeloid leukemia (AML), chronic myeloid leukemia, or myelodysplastic syndrome. 
     
     
       51. The method of  claim 47 , wherein the antibody is administered as part of a combination therapy comprising a PD-1 antagonist. 
     
     
       52. The method of  claim 51 , wherein the PD-1 antagonist is pembrolizumab. 
     
     
       53. An isolated cell comprising a polynucleotide or polynucleotides encoding the antibody of  claim 43  or a vector or vector comprising a polynucleotide or polynucleotides encoding the antibody of  claim 43 .